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Structure of Nelfinavir-resistant HIV-1 protease (D30N/N88D) in complex with Darunavir.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A PDB ENTRY 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 300 126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.09 41.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.858 α = 90 b = 57.703 β = 90 c = 61.614 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2005-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 25 0.067 0.095 9.6 10.5 10326 9.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.23 0.474 0.537 10.4 997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1F7A 2.15 23.97 10293 496 99.22 0.184 0.181 0.1918 0.236 0.2458 RANDOM 35.539
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.18 0.92 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.04 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 10.283 r_scangle_it 2.609 r_angle_refined_deg 1.785 r_scbond_it 1.781 r_mcangle_it 1.295 r_mcbond_it 1.078 r_angle_other_deg 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.04 r_dihedral_angle_4_deg 20.855 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 10.283 r_scangle_it 2.609 r_angle_refined_deg 1.785 r_scbond_it 1.781 r_mcangle_it 1.295 r_mcbond_it 1.078 r_angle_other_deg 0.831 r_mcbond_other 0.212 r_nbd_refined 0.192 r_nbd_other 0.189 r_symmetry_vdw_other 0.173 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.123 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.096 r_nbtor_other 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1485 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling